In the vegetation seasons 2016–2017, a survey of 30 pit lakes localized in the eastern part of the Muskau Arch (Western Poland) was carried out. The aim of the study was to characterize the habitat conditions of the selected lakes, based on the physico-chemical water characteristics. We hypothesized that the age and genesis of pit lakes are the main factors responsible for their hydro-chemical diversity. Therefore, in each of the lakes 27 physico-chemical parameters and chlorophyll a were measured in the water surface, in the peak of the vegetation season (July–August). Additionally, they were described in terms of genesis, origin and age. The results showed that the investigated lakes display a high diversity of habitat conditions reflected in varied physico-chemical water properties (significant lake-to-lake differences). The parameters mostly responsible for the differences were: Secchi depth (transparency), pH, EC, colour, hardness, TP, TN, TC, Ca2+, Mg2+, Fe, Al, Mn, S and Chl a. The comparison of the type of excavated aggregate showed significant differences for four parameters only. Much greater differences were found for the genesis of lakes (mining method) – 15 of the 28 analysed parameters significantly differentiated the lakes. Further analysis showed that half of the studied parameters were significantly correlated with the age of the pit lakes. Our results suggest that in addition to natural changes, secondary human-caused transformations (mostly neutralization and fertilization of the water) were among the key factors responsible for the differentiation of the lakes.